Redundant polygon cleanup tool recommendations?

You don't need an LOD tool or polygon reduction. What you need is less CSG. You'll never manage a clean mesh with something that builds geometry through a boolean operation like CSG does, unless you know exactly how the program likes to cut things up and manage to manipulate it to do exactly what you want. The chances of that are slim. Polygon reduction might leave you with less polygons, but you'll still have a messy mesh, and that can cause issues, depending on what it is you're doing. Whether it does or doesn't, reduction isn't designed for things like levels because it applies the entire reduction to everything all at once.

Your options are, aside from less CSGing, bringing your model into something like Silo and using a retopolgy tool on it to rebuild the mesh correctly. That'd be the best option for organic models, but for levels and the like, you'd be better of building (say for example in 3D World Studio) properly built pre-fab pieces and creating your level with those.

You'll save yourself many headaches.